Eurographics Workshops and Symposia
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Browsing Eurographics Workshops and Symposia by Author "Agus, Marco"
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Item HistoContours: a Framework for Visual Annotation of Histopathology Whole Slide Images(The Eurographics Association, 2022) Al-Thelaya, Khaled; Joad, Faaiz; Gilal, Nauman Ullah; Mifsud, William; Pintore, Giovanni; Gobbetti, Enrico; Agus, Marco; Schneider, Jens; Renata G. Raidou; Björn Sommer; Torsten W. Kuhlen; Michael Krone; Thomas Schultz; Hsiang-Yun WuWe present an end-to-end framework for histopathological analysis of whole slide images (WSIs). Our framework uses deep learning-based localization & classification of cell nuclei followed by spatial data aggregation to propagate classes of sparsely distributed nuclei across the entire slide. We use YOLO (''You Only Look Once'') for localization instead of more costly segmentation approaches and show that using HistAuGAN boosts its performance. YOLO finds bounding boxes around nuclei at good accuracy, but the classification accuracy can be improved by other methods. To this end, we extract patches around nuclei from the WSI and consider models from the SqueezeNet, ResNet, and EfficientNet families for classification. Where we do not achieve a clear separation between highest and second-highest softmax activation of the classifier, we use YOLO's output as a secondary vote. The result is a sparse annotation of the WSI, which we turn dense by using kernel density estimation. The result is a full vector of per pixel probabilities for each class of nucleus we consider. This allows us to visualize our results using both color-coding and isocontouring, reducing visual clutter. Our novel nuclei-to-tissue coupling allows histopathologists to work at both the nucleus and the tissue level, a feature appreciated by domain experts in a qualitative user study.Item InShaDe: Invariant Shape Descriptors for Visual Analysis of Histology 2D Cellular and Nuclear Shapes(The Eurographics Association, 2020) Agus, Marco; Al-Thelaya, Khaled; Cali, Corrado; Boido, Marina M.; Yang, Yin; Pintore, Giovanni; Gobbetti, Enrico; Schneider, Jens; Kozlíková, Barbora and Krone, Michael and Smit, Noeska and Nieselt, Kay and Raidou, Renata GeorgiaWe present a shape processing framework for visual exploration of cellular nuclear envelopes extracted from histology images. The framework is based on a novel shape descriptor of closed contours relying on a geodesically uniform resampling of discrete curves to allow for discrete differential-geometry-based computation of unsigned curvature at vertices and edges. Our descriptor is, by design, invariant under translation, rotation and parameterization. Moreover, it additionally offers the option for uniform-scale-invariance. The optional scale-invariance is achieved by scaling features to z-scores, while invariance under parameterization shifts is achieved by using elliptic Fourier analysis (EFA) on the resulting curvature vectors. These invariant shape descriptors provide an embedding into a fixed-dimensional feature space that can be utilized for various applications: (i) as input features for deep and shallow learning techniques; (ii) as input for dimension reduction schemes for providing a visual reference for clustering collection of shapes. The capabilities of the proposed framework are demonstrated in the context of visual analysis and unsupervised classification of histology images.